This paper proposes three typical multi-channel operation models of pharmaceutical retail chain enterprises taking the relationship between pharmacies and online pharmacies as point of cut-in based on the pharmaceutical retail chain enterprises. We combine actual cases to present the characteristics and its application environments of three typical multi-channel operation modes, respectively. Then, we analyze the main factors which influence multi-channel operation modes according to the reality of pharmaceutical retail market in China, and present relevant strategies and measures from the aspects of enterprise and government, respectively.